I am trying to run the MiModd variant calling tool in galaxy and I got the below error.
I first aligned my fastq file using Bowtie2, while setting a read group ID and sample name. I then used MiModd variant calling tool in attempt to produce a bcf file for MiModd deletion calling. I changed the name of the reference genome but that didn’t help. Anyone got any suggestions? or a better suggestion for finding deletions in my data
Fatal error: Exit code 1 ()
Traceback (most recent call last):
File “/usr/local/tools/_conda/envs/__MiModD@0.1.8/bin/mimodd”, line 7, in
File “/usr/local/tools/_conda/envs/__MiModD@0.1.8/lib/python3.6/site-packages/MiModD/main.py”, line 1197, in parse
result = funcs-1
File “/usr/local/tools/_conda/envs/__MiModD@0.1.8/lib/python3.6/site-packages/MiModD/tmpfiles.py”, line 26, in catch_sigterm_wrapper
ret = f(args, **kwargs)
File “/usr/local/tools/_conda/envs/__MiModD@0.1.8/lib/python3.6/site-packages/MiModD/variant_calling.py”, line 114, in varcall
File “/usr/local/tools/_conda/envs/__MiModD@0.1.8/lib/python3.6/site-packages/MiModD/fasta.py”, line 28, in assert_valid_ids
MiModD.FormatParseError: Invalid reference genome file : Some sequence names contain characters that are not allowed in MiModD.
non-ASCII, whitespace, non-printable characters and any of the characters ",;<=>" are disallowed in sequence names.
You may manually clean up the file or run “python3 -m MiModD.sanitize” to replace invalid characters automatically.